vcf2maf allele frequency not converting

Question

[hamrejr]

Hello,

I have seen this question asked in the past but none of the answers solved my problem. Essentially, I have vcf's, generated by FreeBayes and mutect2, that have the AF in a column with other parameters/ . All I want to do is generate the AF values in one column on the maf.out. Can anyone tell me the commands to do this? I have tried --retain-info, --retain-fmt, and --retain-ann with AF and tAF after each option but nothing has worked. Thanks.

Answer 1

[Pierre Lindenbaum]

not tested but that could be:

paste <(bcftools view in.vcf | grep -v "^#") <(bcftools query -f '%INFO/AF\n' in.vcf)

[hamrejr]

Thanks. I am trying to get this on the maf from the vcf. So the command I am using is:

vcf2maf.pl --input-vcf .vcf --output-maf .vcf.maf --vep-path $VEP_HOME --tumor-id .vcf --vep-data $VEPCACHEDIR --ref-fasta Homo_sapiens_assembly38.fasta --vep-forks 2  --species human --retain-info AB,ABP,AC,tAF --inhibit-vep

However, the columns for AB,ABP,AC,tAF are blank. I am really trying to work with a maf as I have so many samples and need to match columns with merged mafs, as well as get rid of AF's that are above and below a certain threshold for the entire lot.